FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: GYQ11

Calculation Name: 2C0L-A-Xray372

Preferred Name: Non-specific lipid-transfer protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2C0L

Chain ID: A

ChEMBL ID: CHEMBL5950

UniProt ID: P22307

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 292
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4128925.48322
FMO2-HF: Nuclear repulsion 4014545.862778
FMO2-HF: Total energy -114379.620442
FMO2-MP2: Total energy -114712.167979


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:335:HIS)


Summations of interaction energy for fragment #1(A:335:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-195.361-186.40925.381-15.581-18.752-0.142
Interaction energy analysis for fragmet #1(A:335:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.910
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A337GLN00.012-0.0063.0352.0024.6430.010-1.311-1.3390.001
4A338PRO0-0.0040.0032.831-4.217-3.1950.121-0.200-0.944-0.001
5A339PHE00.0560.0384.1731.0501.1760.001-0.017-0.1100.000
6A340GLU-1-0.790-0.9077.606-25.119-25.1190.0000.0000.0000.000
7A341GLU-1-0.885-0.9221.676-117.937-119.85116.895-8.698-6.283-0.102
8A342GLY00.0390.0175.7351.5001.5000.0000.0000.0000.000
9A343LEU00.0150.0068.1142.4842.4840.0000.0000.0000.000
10A344ARG10.8690.9575.40740.61640.6160.0000.0000.0000.000
11A345ARG10.8310.9003.35850.90151.0710.001-0.026-0.1450.000
12A346LEU0-0.008-0.0099.7571.8331.8330.0000.0000.0000.000
13A347GLN0-0.040-0.01712.6832.5852.5850.0000.0000.0000.000
14A348GLU-1-0.940-0.9829.536-29.618-29.6180.0000.0000.0000.000
15A349GLY00.0420.03513.6630.8640.8640.0000.0000.0000.000
16A350ASP-1-0.826-0.8848.866-30.467-30.4670.0000.0000.0000.000
17A351LEU00.0390.00311.123-2.212-2.2120.0000.0000.0000.000
18A352PRO00.0220.01412.273-1.070-1.0700.0000.0000.0000.000
19A353ASN0-0.024-0.0326.801-3.961-3.9610.0000.0000.0000.000
20A354ALA00.0230.0168.249-3.686-3.6860.0000.0000.0000.000
21A355VAL0-0.022-0.0019.851-0.731-0.7310.0000.0000.0000.000
22A356LEU00.0360.0208.217-0.633-0.6330.0000.0000.0000.000
23A357LEU0-0.070-0.0163.235-4.401-3.6940.052-0.152-0.6070.000
24A358PHE00.0120.0016.392-0.543-0.5430.0000.0000.0000.000
25A359GLU-1-0.837-0.9319.214-21.474-21.4740.0000.0000.0000.000
26A360ALA0-0.038-0.0224.6150.5740.654-0.001-0.002-0.0770.000
27A361ALA0-0.054-0.0266.5330.0080.0080.0000.0000.0000.000
28A362VAL00.006-0.0027.7991.4581.4580.0000.0000.0000.000
29A363GLN0-0.038-0.0178.103-0.066-0.0660.0000.0000.0000.000
30A364GLN0-0.091-0.0414.2461.4001.468-0.001-0.008-0.0590.000
31A365ASP-1-0.826-0.9218.755-17.672-17.6720.0000.0000.0000.000
32A366PRO00.0100.01311.8970.2920.2920.0000.0000.0000.000
33A367LYS10.9140.95214.67214.77714.7770.0000.0000.0000.000
34A368HIS00.0720.05510.7151.8291.8290.0000.0000.0000.000
35A369MET0-0.023-0.00114.610-0.373-0.3730.0000.0000.0000.000
36A370GLU-1-0.810-0.91715.145-17.178-17.1780.0000.0000.0000.000
37A371ALA00.0120.00811.068-0.489-0.4890.0000.0000.0000.000
38A372TRP00.012-0.01512.811-0.272-0.2720.0000.0000.0000.000
39A373GLN0-0.0070.00515.7101.2281.2280.0000.0000.0000.000
40A374TYR00.0080.00413.7500.4730.4730.0000.0000.0000.000
41A375LEU0-0.0580.00712.434-0.124-0.1240.0000.0000.0000.000
42A376GLY00.015-0.00414.5270.4740.4740.0000.0000.0000.000
43A377THR0-0.009-0.01218.1600.3560.3560.0000.0000.0000.000
44A378THR00.025-0.00513.6020.2070.2070.0000.0000.0000.000
45A379GLN00.012-0.01415.3600.6050.6050.0000.0000.0000.000
46A380ALA00.0100.01518.0300.6750.6750.0000.0000.0000.000
47A381GLU-1-0.848-0.92918.634-16.314-16.3140.0000.0000.0000.000
48A382ASN0-0.016-0.01116.8290.2280.2280.0000.0000.0000.000
49A383GLU-1-0.806-0.88218.962-12.400-12.4000.0000.0000.0000.000
50A384GLN00.0100.02319.0150.8410.8410.0000.0000.0000.000
51A385GLU-1-0.701-0.80621.495-12.831-12.8310.0000.0000.0000.000
52A386LEU00.0280.01223.797-0.094-0.0940.0000.0000.0000.000
53A387LEU0-0.009-0.00617.675-0.010-0.0100.0000.0000.0000.000
54A388ALA00.0200.01719.497-0.452-0.4520.0000.0000.0000.000
55A389ILE00.0280.01220.682-0.008-0.0080.0000.0000.0000.000
56A390SER0-0.069-0.02420.2250.2910.2910.0000.0000.0000.000
57A391ALA00.0160.00716.9510.0880.0880.0000.0000.0000.000
58A392LEU00.0180.02218.736-0.071-0.0710.0000.0000.0000.000
59A393ARG10.8830.94021.34712.43012.4300.0000.0000.0000.000
60A394ARG10.8250.92518.12915.06815.0680.0000.0000.0000.000
61A395CYS0-0.073-0.02519.0780.1140.1140.0000.0000.0000.000
62A396LEU00.0370.01220.3450.3200.3200.0000.0000.0000.000
63A397GLU-1-0.887-0.94422.980-12.244-12.2440.0000.0000.0000.000
64A398LEU0-0.137-0.05618.4260.1220.1220.0000.0000.0000.000
65A399LYS10.7940.87322.65512.07012.0700.0000.0000.0000.000
66A400PRO00.0370.02024.420-0.081-0.0810.0000.0000.0000.000
67A401ASP-1-0.806-0.88127.344-11.102-11.1020.0000.0000.0000.000
68A402ASN0-0.021-0.03420.9910.2200.2200.0000.0000.0000.000
69A403GLN00.0470.01325.195-0.183-0.1830.0000.0000.0000.000
70A404THR00.0270.02021.2290.3890.3890.0000.0000.0000.000
71A405ALA00.019-0.00421.687-0.077-0.0770.0000.0000.0000.000
72A406LEU0-0.035-0.00923.2930.1560.1560.0000.0000.0000.000
73A407MET00.0190.02226.7500.2770.2770.0000.0000.0000.000
74A408ALA00.001-0.00223.1190.1600.1600.0000.0000.0000.000
75A409LEU0-0.0110.00025.0280.0900.0900.0000.0000.0000.000
76A410ALA00.0280.01126.3760.3090.3090.0000.0000.0000.000
77A411VAL0-0.0080.01027.2730.3480.3480.0000.0000.0000.000
78A412SER0-0.013-0.02425.0380.1000.1000.0000.0000.0000.000
79A413PHE0-0.023-0.03627.5350.1550.1550.0000.0000.0000.000
80A414THR0-0.005-0.01730.6020.4620.4620.0000.0000.0000.000
81A415ASN0-0.070-0.04027.7260.5520.5520.0000.0000.0000.000
82A416GLU-1-0.941-0.97129.245-10.663-10.6630.0000.0000.0000.000
83A417SER0-0.025-0.01132.0310.3600.3600.0000.0000.0000.000
84A418LEU0-0.053-0.00931.2850.3160.3160.0000.0000.0000.000
85A419GLN00.0320.01435.013-0.034-0.0340.0000.0000.0000.000
86A420ARG10.8220.90137.2557.8027.8020.0000.0000.0000.000
87A421GLN00.0750.03232.6750.1020.1020.0000.0000.0000.000
88A422ALA00.0280.02032.570-0.228-0.2280.0000.0000.0000.000
89A423CYS0-0.020-0.00333.621-0.009-0.0090.0000.0000.0000.000
90A424GLU-1-0.872-0.95235.187-8.432-8.4320.0000.0000.0000.000
91A425ILE0-0.013-0.00129.044-0.024-0.0240.0000.0000.0000.000
92A426LEU00.0280.01732.011-0.140-0.1400.0000.0000.0000.000
93A427ARG10.7660.85533.8497.8597.8590.0000.0000.0000.000
94A428ASP-1-0.813-0.88632.128-9.006-9.0060.0000.0000.0000.000
95A429TRP00.0060.00328.9160.1080.1080.0000.0000.0000.000
96A430LEU0-0.0070.01531.997-0.027-0.0270.0000.0000.0000.000
97A431ARG10.7810.85434.8158.9168.9160.0000.0000.0000.000
98A432TYR0-0.029-0.01430.9450.1940.1940.0000.0000.0000.000
99A433THR00.0310.01631.869-0.366-0.3660.0000.0000.0000.000
100A434PRO0-0.044-0.03932.1960.3170.3170.0000.0000.0000.000
101A435ALA0-0.0200.00235.2860.2360.2360.0000.0000.0000.000
102A436TYR0-0.021-0.05635.4200.3490.3490.0000.0000.0000.000
103A437ALA00.0340.03936.9780.1490.1490.0000.0000.0000.000
104A438HIS0-0.034-0.00938.6130.0290.0290.0000.0000.0000.000
105A439LEU0-0.0210.00640.8530.2120.2120.0000.0000.0000.000
106A440VAL0-0.120-0.06639.1060.1890.1890.0000.0000.0000.000
107A454PRO00.0320.00849.4040.0090.0090.0000.0000.0000.000
108A455SER00.0450.00549.019-0.137-0.1370.0000.0000.0000.000
109A456LYS10.9930.99250.2695.8365.8360.0000.0000.0000.000
110A457ARG11.0211.02843.1977.1327.1320.0000.0000.0000.000
111A458ILE0-0.037-0.01045.234-0.135-0.1350.0000.0000.0000.000
112A459LEU00.0240.00046.044-0.101-0.1010.0000.0000.0000.000
113A460GLY00.0300.02247.237-0.019-0.0190.0000.0000.0000.000
114A461SER0-0.006-0.01641.810-0.125-0.1250.0000.0000.0000.000
115A462LEU00.0090.01042.591-0.162-0.1620.0000.0000.0000.000
116A463LEU0-0.0100.00144.7810.0010.0010.0000.0000.0000.000
117A464SER00.028-0.00241.568-0.069-0.0690.0000.0000.0000.000
118A465ASP-1-0.831-0.91643.048-7.052-7.0520.0000.0000.0000.000
119A466SER0-0.082-0.03745.6550.0990.0990.0000.0000.0000.000
120A467LEU0-0.047-0.01239.1140.0110.0110.0000.0000.0000.000
121A468PHE00.0410.01340.560-0.066-0.0660.0000.0000.0000.000
122A469LEU0-0.021-0.00142.295-0.076-0.0760.0000.0000.0000.000
123A470GLU-1-0.791-0.86943.773-7.260-7.2600.0000.0000.0000.000
124A471VAL0-0.007-0.00937.734-0.014-0.0140.0000.0000.0000.000
125A472LYS10.8750.94540.8067.1227.1220.0000.0000.0000.000
126A473GLU-1-0.934-0.98042.151-6.596-6.5960.0000.0000.0000.000
127A474LEU0-0.064-0.02241.3930.0500.0500.0000.0000.0000.000
128A475PHE00.0330.00834.510-0.050-0.0500.0000.0000.0000.000
129A476LEU0-0.013-0.00940.4160.0200.0200.0000.0000.0000.000
130A477ALA0-0.087-0.04643.6060.1040.1040.0000.0000.0000.000
131A478ALA00.0290.00939.4040.0660.0660.0000.0000.0000.000
132A479VAL00.0000.00240.143-0.002-0.0020.0000.0000.0000.000
133A480ARG10.8990.94342.2516.8866.8860.0000.0000.0000.000
134A481LEU0-0.057-0.01641.8030.1750.1750.0000.0000.0000.000
135A482ASP-1-0.785-0.84542.435-7.307-7.3070.0000.0000.0000.000
136A483PRO0-0.037-0.00343.184-0.121-0.1210.0000.0000.0000.000
137A484THR0-0.131-0.08645.0210.0650.0650.0000.0000.0000.000
138A485SER0-0.073-0.05339.707-0.148-0.1480.0000.0000.0000.000
139A486ILE00.013-0.00436.6880.0660.0660.0000.0000.0000.000
140A487ASP-1-0.750-0.83634.064-9.621-9.6210.0000.0000.0000.000
141A488PRO00.013-0.01131.1390.1230.1230.0000.0000.0000.000
142A489ASP-1-0.787-0.87129.141-11.193-11.1930.0000.0000.0000.000
143A490VAL00.006-0.00131.9910.0310.0310.0000.0000.0000.000
144A491GLN00.0090.00635.4340.1190.1190.0000.0000.0000.000
145A492CYS0-0.043-0.01130.556-0.055-0.0550.0000.0000.0000.000
146A493GLY00.0240.00233.1340.0030.0030.0000.0000.0000.000
147A494LEU0-0.034-0.01534.1800.1630.1630.0000.0000.0000.000
148A495GLY00.0480.02136.1500.2100.2100.0000.0000.0000.000
149A496VAL0-0.020-0.00931.7020.0430.0430.0000.0000.0000.000
150A497LEU0-0.004-0.01435.0450.1690.1690.0000.0000.0000.000
151A498PHE0-0.031-0.03138.1980.2390.2390.0000.0000.0000.000
152A499ASN0-0.032-0.03836.3310.1010.1010.0000.0000.0000.000
153A500LEU0-0.045-0.01335.6560.1020.1020.0000.0000.0000.000
154A501SER0-0.052-0.05839.1240.0870.0870.0000.0000.0000.000
155A502GLY00.0380.02741.8440.1940.1940.0000.0000.0000.000
156A503GLU-1-0.821-0.84343.279-7.078-7.0780.0000.0000.0000.000
157A504TYR00.0580.00638.758-0.047-0.0470.0000.0000.0000.000
158A505ASP-1-0.846-0.93041.157-7.243-7.2430.0000.0000.0000.000
159A506LYS10.8600.91942.9916.9116.9110.0000.0000.0000.000
160A507ALA00.0020.00637.828-0.111-0.1110.0000.0000.0000.000
161A508VAL00.0100.01137.984-0.262-0.2620.0000.0000.0000.000
162A509ASP-1-0.888-0.92038.624-7.614-7.6140.0000.0000.0000.000
163A510CYS0-0.069-0.02237.834-0.050-0.0500.0000.0000.0000.000
164A511PHE00.013-0.01532.574-0.264-0.2640.0000.0000.0000.000
165A512THR0-0.017-0.01834.577-0.265-0.2650.0000.0000.0000.000
166A513ALA0-0.009-0.00136.770-0.057-0.0570.0000.0000.0000.000
167A514ALA00.0100.01332.605-0.070-0.0700.0000.0000.0000.000
168A515LEU0-0.012-0.01130.460-0.226-0.2260.0000.0000.0000.000
169A516SER0-0.104-0.06133.235-0.017-0.0170.0000.0000.0000.000
170A517VAL0-0.029-0.00332.3950.0500.0500.0000.0000.0000.000
171A518ARG10.7050.80227.09011.07711.0770.0000.0000.0000.000
172A519PRO00.0560.03529.704-0.250-0.2500.0000.0000.0000.000
173A520ASN00.003-0.00225.8810.1660.1660.0000.0000.0000.000
174A521ASP-1-0.765-0.87625.312-12.750-12.7500.0000.0000.0000.000
175A522TYR00.006-0.03318.9550.4850.4850.0000.0000.0000.000
176A523LEU00.0300.02221.5350.2870.2870.0000.0000.0000.000
177A524LEU0-0.076-0.02425.5010.3500.3500.0000.0000.0000.000
178A525TRP00.0150.00028.3120.4910.4910.0000.0000.0000.000
179A526ASN00.0540.02826.1370.5900.5900.0000.0000.0000.000
180A527LYS10.8740.94527.02711.65511.6550.0000.0000.0000.000
181A528LEU00.0020.02231.0620.3160.3160.0000.0000.0000.000
182A529GLY00.0510.00632.4370.2920.2920.0000.0000.0000.000
183A530ALA00.0080.00431.3470.2330.2330.0000.0000.0000.000
184A531THR0-0.011-0.01133.3460.2870.2870.0000.0000.0000.000
185A532LEU0-0.029-0.00336.2820.2810.2810.0000.0000.0000.000
186A533ALA0-0.009-0.00635.2620.2230.2230.0000.0000.0000.000
187A534ASN0-0.024-0.00735.0870.1920.1920.0000.0000.0000.000
188A535GLY0-0.031-0.01238.6480.2140.2140.0000.0000.0000.000
189A536ASN0-0.064-0.03740.8020.1130.1130.0000.0000.0000.000
190A537GLN0-0.053-0.01340.6780.2760.2760.0000.0000.0000.000
191A538SER00.0740.01438.160-0.283-0.2830.0000.0000.0000.000
192A539GLU-1-0.921-0.94537.454-8.320-8.3200.0000.0000.0000.000
193A540GLU-1-0.872-0.95637.772-7.941-7.9410.0000.0000.0000.000
194A541ALA0-0.013-0.00834.966-0.245-0.2450.0000.0000.0000.000
195A542VAL00.0080.00533.524-0.406-0.4060.0000.0000.0000.000
196A543ALA0-0.017-0.00432.850-0.327-0.3270.0000.0000.0000.000
197A544ALA0-0.0060.00632.864-0.254-0.2540.0000.0000.0000.000
198A545TYR00.009-0.00429.037-0.460-0.4600.0000.0000.0000.000
199A546ARG10.8210.89428.1819.3619.3610.0000.0000.0000.000
200A547ARG10.8570.91728.3979.7219.7210.0000.0000.0000.000
201A548ALA00.004-0.01326.125-0.375-0.3750.0000.0000.0000.000
202A549LEU0-0.056-0.02623.227-0.634-0.6340.0000.0000.0000.000
203A550GLU-1-0.878-0.91923.964-10.728-10.7280.0000.0000.0000.000
204A551LEU0-0.079-0.02524.411-0.297-0.2970.0000.0000.0000.000
205A552GLN00.0150.01317.443-0.638-0.6380.0000.0000.0000.000
206A553PRO00.0510.02819.779-0.022-0.0220.0000.0000.0000.000
207A554GLY00.0280.02717.1760.2720.2720.0000.0000.0000.000
208A555TYR0-0.036-0.00618.063-0.289-0.2890.0000.0000.0000.000
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